Variant report

Variant	rs3812822
Chromosome Location	chr12:4489235-4489236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr12:4488369-4489237	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:4489221-4489271	HRPEpiC	eye:	n/a
2	chr12:4489221-4489271	HUVEC	blood vessel:	n/a
3	chr12:4489221-4489271	HNPCEpiC	eye:	n/a
4	chr12:4489221-4489271	HRE	kidney:	n/a
5	chr12:4489221-4489271	HMEC	breast:	n/a
6	chr12:4489221-4489271	Jurkat	blood:	n/a
7	chr12:4489221-4489271	LNCaP	prostate:	n/a
8	chr12:4489221-4489271	T-47D	breast:	n/a
9	chr12:4489221-4489271	ECC-1	luminal epithelium:	n/a
10	chr12:4489221-4489271	GM19239	blood:	n/a
11	chr12:4489221-4489271	AG04450	lung:	fetal
12	chr12:4489221-4489271	U87	brain:	n/a
13	chr12:4489221-4489271	HAEpiC	amniotic membrane:	n/a
14	chr12:4489221-4489271	PrEC	prostate:	n/a
15	chr12:4489221-4489271	NT2-D1	testis:	n/a
16	chr12:4489221-4489271	HPAEpiC	pulmonary alveolar:	n/a
17	chr12:4489221-4489271	NHBE	bronchial:	n/a
18	chr12:4489221-4489271	AG04449	skin:	fetal
19	chr12:4489221-4489271	GM12878	blood:	n/a
20	chr12:4489221-4489271	NB4	blood:	n/a
21	chr12:4489221-4489271	HEK293	kidney:	embryo
22	chr12:4489221-4489271	AG09319	gingival:	n/a
23	chr12:4489221-4489271	SKMC	muscle:	n/a
24	chr12:4489221-4489271	MCF10A-Er-Src	breast:	n/a
25	chr12:4489221-4489271	PANC-1	pancreas:	n/a
26	chr12:4489221-4489271	Hela-S3	cervix:	n/a
27	chr12:4489221-4489271	PFSK-1	brain:	n/a
28	chr12:4489221-4489271	HRCEpiC	kidney:	n/a
29	chr12:4489221-4489271	AG09309	skin:	n/a
30	chr12:4489221-4489271	SK-N-MC	brain:	n/a
31	chr12:4489221-4489271	NHDF-neo	bronchial:	n/a
32	chr12:4489221-4489271	AoSMC	blood vessel:	n/a
33	chr12:4489221-4489271	SK-N-SH	brain:	n/a
34	chr12:4489221-4489271	GM06990	blood:	n/a
35	chr12:4489221-4489271	AG10803	skin:	n/a
36	chr12:4489221-4489271	BJ	skin:	n/a
37	chr12:4489221-4489271	A549	lung:	n/a
38	chr12:4489221-4489271	HepG2	liver:	n/a
39	chr12:4489221-4489271	HL-60	blood:	n/a
40	chr12:4489221-4489271	ovcar-3	ovarian:	n/a
41	chr12:4489221-4489271	HCF	heart:	n/a
42	chr12:4489221-4489271	MCF-7	breast:	n/a
43	chr12:4489221-4489271	H1-hESC	embryonic stem cell:	embryo
44	chr12:4489221-4489271	IMR90	lung:	fetal
45	chr12:4489221-4489271	HIPEpiC	eye:	n/a
46	chr12:4489221-4489271	HEEpiC	esophagus:	n/a
47	chr12:4489221-4489271	HCPEpiC	choroid plexus:	n/a
48	chr12:4489221-4489271	BE2_C	brain:	n/a
49	chr12:4489221-4489271	Hepatocyte	liver:	n/a
50	chr12:4489221-4489271	HCT-116	colon:	n/a

No data

Variant related genes	Relation type
FGF23	TF binding region
FGF23	CpG island

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11063105	0.88[ASN][1000 genomes]
rs11063110	0.88[ASN][1000 genomes]
rs11063112	0.94[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs11063116	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11063118	0.88[CHB][hapmap]
rs11063123	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11063127	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063129	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063130	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230757	0.87[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs12823931	0.87[CHB][hapmap]
rs13312789	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16931344	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17773299	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2358955	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61909253	0.84[ASN][1000 genomes]
rs61909254	0.84[ASN][1000 genomes]
rs6489538	1.00[ASN][1000 genomes]
rs7316649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955866	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7961824	0.86[ASN][1000 genomes]
rs7966472	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7967051	0.98[ASN][1000 genomes]
rs7976548	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7978281	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3812822	NECAP1	cis	cerebellum	SCAN
rs3812822	CDCA3	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4488800-4489800	Enhancers	Fetal Intestine Large	intestine
2	chr12:4488800-4489800	Enhancers	Fetal Intestine Small	intestine
3	chr12:4488800-4493400	Weak transcription	Brain Germinal Matrix	brain
4	chr12:4489000-4489400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
5	chr12:4489000-4492400	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links